Automated

ImageJ native "Skeletonize" implementation. - works only with 8-bit binary image. A faster implementation is available as a plugin Skeletonize3D written by Ignacio Arganda-Carreras. Pros of this plugin is summarized here.

Quote:

The "Angiogenesis Analyzer" allows analysis of cellular networks. Typically, it can detect and analyze the pseudo vascular organization of endothelial cells cultured in gel medium

...a simple tool to quantify the ETFA (Endothelial Tube Formation Assay) experiment images by extracting characteristic information of the network.

The outputs are network feature parameters.

Sample images

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Pseudo-Phase-Contrast.tif.zip

http://image.bio.methods.free.fr/ij/ijmacro/Angiogenesis/HUVEC-Fluo.tif.zip

Source code

https://imagej.nih.gov/ij/macros/toolsets/Angiogenesis%20Analyzer.txt

Evaluates the orientation of fiber orientation pattern and plots the results in the image. It calculates gradient in x and y direction. - then calculates the eigenvector of nematic tensor, which is the orientation of the pattern.

## Short Summary Quote from the plugin page: >LineageTracker offers an ImageJ based framework which is easily extendible and has the capability to track cell lineages while being specifically designed to handle large cell displacements between frames. The methods are designed for fluorescent cells and have been used to analyse Schizosaccharomyces pombe, C2C12 mouse stem cells or migrating RPE cells. This tool also allows flexible cell segmentation and extendable in all aspects. The webpage is detailed with usage from ImageJ macro. Rather than being simply a component, the plugin is indeed a framework with set of components. ## Misc info A tip from the plugin author in ImageJ mailing list (08.Sep.2015): > We have an additional script to export only a selected range of frames. I can send you that if you think LineageTracker is something for you. To be on the safe side I would try it with an older version of ImageJ. We have experienced some problems, mostly related to Java. Java 8 seems to fix most of it. ## References 2630: Application example. 2631: Plugin Paper.

The GDSC Single Molecule Light Microscopy (SMLM) plugins is a package of tools for single molecule localisation analysis. - Fitting Plugins: get point cloud from super resolution image. - Results Plugins: organize results. - Analysis plugins - Model plugins